Hpv vaccine comprising peptides from host cell proteins

ABSTRACT

The present invention relates to a human papillomavirus (HPV) vaccine that comprises peptides from host cell proteins and more particularly, a vaccine that is directed against cancers that are associated with HPV infections, such as cervical cancer, head and neck cancer and skin cancers. The peptides comprise fragments of host cell proteins that have been targeted for degradation by HPV proteins, such as E6 and E7 and are presented on the surface of HPV infected cells in relatively large amounts. These peptides can be recognised by CTL and elicit an immune response, and are therefore ideal tumour-specific markers. The invention also relates to novel peptide: peptide complexes such as peptide/HLA complexes and their use in a tumour-specific vaccine.

This application is a continuation-in-part of international applicationnumber PCT/GB2005/002962 (publication no. WO 2006/013336) filed on Jul.27, 2005 and entitled HPV VACCINE COMPRISING PEPTIDES FROM HOST CELLPROTEINS and claims the benefit of the above-mentioned internationalapplication and the corresponding British national patent applicationno. GB 0417430.6 filed on Aug. 5, 2004 and entitled A NOVEL HPV VACCINECOMPRISING PEPTIDES FROM HOST CELL PROTEINS, the disclosures of each ofwhich are incorporated herein in their entirety by reference.

FIELD OF THE INVENTION

The present invention relates to a human papillomavirus (HPV) vaccinethat comprises peptides from host cell proteins and more particularly,but not exclusively, to a vaccine that is directed against cancers thatare associated with HPV infections, such as cervical cancer, head andneck cancer and skin cancers. The peptides comprise fragments of hostcell proteins that have been targeted for degradation by HPV proteins,such as E6 and E7. Further, the invention relates to the identificationof novel peptides and uses thereof. Additionally, the invention relatesto novel peptide: peptide complexes and uses thereof.

BACKGROUND TO THE INVENTION

Human papillomavirus (HPV) is a very common virus that causes abnormalgrowth of tissue on the feet, hands, vocal cords, mouth and genitalorgans. Over 60 types of HPV have been identified and each type infectscertain parts of the body. HPV is mainly spread through physical contactwith an infected individual. In the majority of cases, HPV disappearswithin 1-2 years and indeed, during the course of the infection, may besubclinical; the individual may be unaware of their infection. However,in a small number of cases, HPV can progress and develop into cancer.

There are two kinds of abnormal tissue caused by HPV: condyloma (warts)and dysplasia (pre-cancer). Wart-like growths can be found in anyinfected areas and may cause itching, burning or slight bleeding. Inthese instances, antiviral creams may be prescribed or, in some cases,the growth may be removed or destroyed by cold cautery (freezing thatdestroys tissue) or hot cautery (burning warts off with an electricinstrument or laser treatment).

Where HPV infection progresses to cancer, cancer patients are treated bya combination of surgery, radiotherapy and chemotherapy. However,radiotherapy and chemotherapy have the disadvantage of destroyinghealthy as well as malignant cells, and can thus cause severe sideeffects, while surgery is invasive and leaves the patient open tosecondary infections. These side effects and risks are undesirable, andcoupled to this is the fact that these treatments are not alwayssuccessful, resulting in the majority of patients entering relapse andso representing with the disease.

It is therefore clear that more effective treatments are required, andit has been suggested that the specificity of the immune system might beharnessed against virally infected cells. This concept has been termed“immunotherapy”.

In particular, it has been shown that cancer patients have T cells thatare capable of recognising their tumour cells, but these cells do notdivide and differentiate into cytotoxic T lymphocytes (CTL) which arecapable of killing these cells.

Cytotoxic T lymphocytes kill “target” cells, such as virally-infectedcells, and have also been implicated in the “immune surveillance” ofcancer cells. The majority of CTL belong to the CD8⁺-subset of T cellsand have T-cell receptors (TCR). These TCR are able to recognisepeptides when they are expressed on the surface of cells in associationwith class 1 major histocompatibility complex (MHC) molecules. In man,each class of MHC is represented by more than one locus; these arecalled human leucocyte antigen (HLA). The class 1 HLA loci are HLA-A,-B, -C, -E, -F and -G. Additionally each HLA has different alleles andTable 1 lists those alleles that have been identified to date.

When a CTL encounters an antigen/MHC complex for which its TCR isspecific, it enters the cell cycle and goes through several rounds ofmitosis, followed by differentiation into an effector/killer cell.Differentiation includes forming a large number of modified lysosomesthat contain the cell-killing proteins perforin and granzyme. Once theCTL have killed the target cells most of them will die, although a smallproportion become memory cells that can respond to the antigen quicklyif it reappears.

Tumour-reactive cytotoxic T lymphocytes have been shown to mediatetumour regression in animal models (1) and in man (2), and there hasthus been an interest in using tumour-specific CTL's as an immunotherapyfor human cancers.

In this regard monoclonal antibodies have been shown to be effectiveagainst some cancers, especially cancers of white blood cells, and aretargeted at a molecule or receptor that is associated with cancer cells.Table 2 lists some of these antibodies and their mechanism of action.

Alternatively, dendritic-cell vaccines have been used to elicit atumour-specific CTL response. Dendritic cells are the most potentantigen-presenting cells and they act by engulfing antigen, processingit into peptides and presenting it to T cells. To make a dendritic-cellvaccine, dendritic cells are harvested, exposed in vitro to antigenassociated with the type of tumour in the patient, and then re-injectedinto the patient. To date these vaccines have shown some promise againstmelanoma, prostrate cancer and lymphoma.

Ideally these vaccines target molecules that are expressed on cancercells, but not on healthy cells. However such tumour-specific antigenshave been hard to find, and as a result many of the immune agents now inuse also target healthy cells in the hope that these cells, eventually,will be replaced. As with radiotherapy and chemotherapy, this treatmentcan cause severe side effects and also leads to the potential forautoimmunity (3). Indeed, in the case of a telomerase vaccine, thisprotein is also present in the stem cells of bone marrow, reproductiveorgans and perhaps other tissues. Further, the antigen to which somedendritic cells are exposed include tyrosinase, which is to be found inmelanocytes, or prostatic acid phosphatase (PAP), which is to be foundin prostate cells.

It is therefore clear that additional viral therapies are needed,particularly for those patients with an advanced stage disease that hasfailed to respond to conventional viral or cancer treatments.

Recently, a number of studies have shown that high-level expression ofcertain proteins in tumour cells is sufficient to allow CTL todiscriminate between tumours and normal cells (4,5).

One way of avoiding autoimmunity in tumour immunotherapy is to targetthe 15% of human malignancies that are associated with viruses. Of thesethe strongest association is between cervical cancer and humanpapillomarivus, with 99.7% of cervical cancers containing HPV DNA (6).There are over 25 HPVs that infect the genital mucosa and give rise tomalignancies such as cervical cancer, head and neck cancers and skincancers. These “high risk” HPVs are characterised by at least twooncogene products: E6 and E7, which act to immortalise and transform, inthe cervix, epithelial cells. The expression of these proteins isthought to be essential to retain the transformed phenotype of thecancer cell and so these non-self viral proteins are thereforeattractive targets for CTL mediated immunotherapy.

CTL active against HPV E6/E7 can be induced by vaccination (7) and suchCTL have been detected with variable frequency in patients withpremalignant cervical disease (8) or cancer (9). However it has beendifficult to generate these CTL in vitro, probably because they occur atlow frequency (10). A major limitation of using these proteins astumour-specific targets is that they are expressed at low levels incancer cells (11). Furthermore, the E6 and E7 proteins themselves aresmall and contain few epitopes suitable for recognition by CTL (12).

The present invention aims to overcome these problems by identifying andthen targeting peptides that are recognised by CTL, which peptides arespecific to HPV transformed cells and are very unlikely to give rise toautoimmunity. These peptides are either uniquely presented orover-presented in HPV transformed cells, and the proteins from whichthese peptides are derived are, typically, either absent or appear to beexpressed at very low levels in HPV transformed cells. In contrast,these proteins occur at normal or high levels in normal cells.

The invention is based on the mechanism that HPV E6 and E7 oncoproteinsuse to mediate targeted degradation of host cell proteins such asretinoblastoma proteins (Rb), C-MYC and HMCM7, among others (see Table3), which takes place during transformation of the infected cell.

It is well known that HPV oncoproteins bind to and facilitate thedegradation of host cell proteins, such as Rb. Thus, analysis of HPVtransformed cervical carcinomas reveals no apparent expression offull-length Rb protein, whereas normal cells have high cellular levelsof the Rb protein, as this is not normally proteolytically degraded(13).

It has been shown that Rb proteins are degraded by theubiquitin-dependant proteolysis system (13), and more recently, it hascome to light that intracellular organelles called proteasomes play arole in mediating degradation (18,19) of host cell proteins afterinteraction with E6 or E7 oncoproteins.

We have recognised the fact that the degradation of, for exampleubiquinated protein substrates by proteasomes, is possibly the majormechanism by which peptides recognised by CTL's are generated (20, 21).For example, in a virally infected cell, newly synthesised viralproteins in the cytoplasm are degraded by proteasomes into peptidefragments. These peptides are transported into the endoplasmic reticulum(ER) by transporter associated with antigen processing (TAP) proteins.Once inside the ER, the peptides will bind to free MHC class I moleculesand beta 2 microglobulin to form a mature MHC/peptide complex. This istransported to the cell surface where it may be recognised by CTL. FIG.1 shows a diagrammatic representation of this process.

Accordingly, the present invention is based on the theory that in HPVtransformed cells, Rb proteins (and other proteins, see Table 3) will betargeted for degradation, processed and peptides thereof will bepresented on the surface of the cell as peptides that can be recognisedby CTL. In non-HPV transformed, or normal, cells these proteins will notbe degraded significantly, so these peptides, effectively, will not beavailable for CTL recognition. Thus, HPV transformed cells should havehigh levels of, for example, Rb derived peptides typically co-presentedon the cell surface in a peptide HLA complex, but low intracellularlevels of the full-length proteins, contrary to normal cells (FIG. 2).

The use of host cell proteins as targets for immunotherapy is not novel.However, in all previous instances this approach has relied on theover-expression of proteins in tumours, compared to normal cells. Forexample, host cell proteins such as p53 (5), Wilms transcription factor(WT1), Her 2/Neu (16) and hTert (17) have been proposed as“tumour-specific” antigens, as all of these are over-expressed in tumourcells. To our knowledge, this is the first time that a HPV or cancervaccine has been directed at “tumour-specific” proteins, and moreparticularly peptides thereof, that are expressed at normal, low, orundetectable levels in HPV transformed cells, compared to normal cells.

Previously, high levels of antigen expression were thought advantageousin order to allow CTL to discriminate between tumour cells and normalcells.

Additionally, up until now HPV vaccines have comprised proteins that areproduced by HPV, not host proteins that are targeted for degradation bythis virus.

In summary, the current invention relies on a relatively high level ofpresentation of peptides at the cell surface but not necessarily onrelatively high levels of expression, or apparent expression, of thecorresponding proteins in the virally-infected cell. In fact, low levelor no expression of the tumour-specific protein would typically indicatethat the protein was being targeted for degradation by viral proteinsand so was present at low intracellular levels, but followingdegradation, presented at the cell membrane and so was available as apeptide for CTL recognition.

Accordingly, in one aspect of the invention, there is therefore provideda vaccine comprising: at least one isolated, purified, synthesised orrecombinant peptide, wherein the peptide is a fragment of a host cellprotein that has been degraded by human papillomavirus oncoproteins, andcan elicit a CTL response when administered to a mammal.

Reference herein to a cell protein that has been degraded by humanpapillomavirus oncoproteins includes reference to a protein that hasbeen selectively targeted for degradation by HPV oncoproteins and soincludes a protein that, in a HPV transformed cell, would be selectivelytargeted for degradation or a protein that is acted upon by human HPVoncoproteins in such a way that it is, directly or indirectly, degraded,most typically but not exclusively, by the ubiquitin pathway.

In a preferred embodiment of the invention the mammal is human.

Preferably, the oncoprotein is E6 or E7.

The host cell protein may be any protein that is degraded by viralproteins, such as E6 or E7, and Table 3 lists those proteins that arecurrently known to be targeted for degradation by E6 or E7.

Preferably, the peptide is HPV-specific or tumour-specific, meaning thatit is presented in high amounts on the cell surface of HPV transformedor tumour cells, relative to normal cells.

Even more preferably, the peptide is 9 to 30 amino acids in length.

Alternatively, the peptide may be 9 to 11 amino acids in length.

The CTL response is preferably a HPV-specific or tumour-specific CTLresponse, meaning that the CTL can recognise HPV transformed cells ortumour cells expressing the peptides of the vaccine.

More preferably, the vaccine comprises one or more of the peptides shownin Table 4 (SEQ ID NOS: 1-163).

More preferably still, the vaccine comprises any of the aforementionedpeptides plus a further protein or peptide comprising a majorhistocompatibility complex molecule, ideally, a class I molecule andmore specifically a human leucocyte antigen (HLA), and more ideallystill a HLA selected from Table 1.

In another aspect of the invention, there is provided a vaccinecomprising: at least one isolated, purified, synthesised or recombinantpeptide, wherein the peptide is chosen from those listed in Table 4.

In yet another aspect of the invention, there is provided a vaccinecomprising: at least one isolated, purified, synthesised or recombinantpeptide selected from Table 4 and, further at least one isolated,purified, synthesised or recombinant HLA selected from those listed inTable 1.

In a further aspect of the invention, there is provided a vaccinecomprising: at least one isolated, purified, synthesised or recombinantnucleic acid molecule encoding any peptide or peptide/HLA complex asdescribed above.

In this embodiment, the nucleic acid molecule may be in the form of avector that comprises a recombinant construct. Ideally the construct isadapted for the expression of said vaccine in a selected host system.The host system is a cell, plasmid, virus, live organism or othersimilar vehicle.

According to a further aspect of the invention there is provided a hostcell transformed or transfected with the vector of the invention.

Additionally, the present invention provides a method of manufacturing avaccine, which method comprises; culturing a host cell transformed ortransfected with a vector comprising a recombinant construct asdescribed above; and isolating/purifying the resulting constructproduct.

The peptides of the present invention may also be used to generate andisolate HPV-specific or tumour-specific cytotoxic T lymphocytes or theirT cell receptors or the genes encoding said receptors, in vitro, for usein adoptive immunotherapy. This could for example be carried out byculturing T lymphocytes with at least one of the peptides describedabove.

According to yet a further aspect of the invention there is provided amethod of identifying HPV-specific or tumour-specific cytotoxic Tlymphocytes comprising:

(a) culturing a sample containing cytotoxic T lymphocytes with at leastone peptide that represents a fragment of a host cell protein which isdegraded by HPV proteins when said host cell is transformed ortransfected by HPV whereby said peptide is ultimately presented on asurface of a virally infected cell; and

(b) selecting CTL that recognise said peptide by binding thereto.

In a preferred method of the invention said peptide is one selected fromthe list shown in Table 4. In yet a further preferred method of theinvention the CTL are CD8⁺ cells.

It will be apparent to those skilled in the art that CTL receptors mayfurther be identified using the aforementioned method.

The present invention can be used to treat HPV associated diseases andparticularly cancer, preferably cervical cancer, head and neck squamouscell cancer, non-melanoma skin cancers, liver cancer, mesothioloma orprostrate cancer.

Furthermore, the present invention also provides a method of treatment,which method comprises administering a vaccine as described above, to amammal to be treated. Ideally, the mammal is human.

According to a further aspect of the invention there is provided apeptide, or a nucleic acid molecule encoding same, selected from thelist shown in Table 4.

In a further embodiment of the invention, said peptide is for use as avaccine and in particular for use as a HPV vaccine to treat HPVassociated disorders.

According to a further aspect of the invention there is provided acomplex comprising at least one of the peptides listed in Table 4 inassociation with a HLA co-presenting peptide.

More preferably the HLA peptide is one of the peptides listed in Table 1and more specifically HLA-A binding protein and more specifically stillHLA-A 0201.

According to a further aspect of the invention there is provided the useof a HPV-specific peptide for the production of a HPV vaccine whereinsaid peptide is a fragment of a mammalian cell protein that has beendegraded by human papillomavirus oncoproteins and which is presented, incombination with HLA, at the surface of the transformed or transfectedHPV cell whereby the recognition of this peptide HLA complex by acytotoxic T lymphocyte results in the elicitation of an immune response.

The invention will now be described by way of the following examples andwith reference to the following Figures wherein:

FIG. 1 shows a mechanism for T cell recognition of host cell proteins incells transformed by human papillomavirus;

FIG. 2 shows a difference in presentation of host cell peptides innormal and HPV transformed cells;

FIG. 3 shows HLA-A2 binding of host protein derived peptides.Specifically, HLA-A*0201 expression of T2 cells was monitored by flowcytometry after overnight incubation with 100 μg test peptides. Eachpeptide was tested in quadruplicate. A % increase in HLA-A*0201expression of above 50% was considered significant;

FIG. 4 shows generation of T cell responses in vivo against a peptidederived from human Rb protein. Specifically, HLA-A2/Kb transgenic micewere immunised with 100 μg of test peptide emulsified in incompletefreunds adjuvant. Two to four mice were tested for each peptide. Ten toeleven days later, mice were sacrificed and splenocytes tested inELISPOT assays. These measured the numbers of IFN□ producing T cells(spots) specific for the immunising peptide. Positive results wereconfirmed in at least two further repeat experiments. Representativedata from 1 experiment testing M1₅₈₋₆₆, Rb1, Rb7 and BAK18 peptides, areshown;

FIG. 5 shows CD8⁺ T cells recognising Rb7 can be detected in healthyHLA-A2⁺ donors. Specifically, CD8+ T cells were cultured with Rb7(panels C&D) or Melan-A/Mart1₂₆₋₃₅ (panels A&B) peptides for 14 days. Onday 0 and day 14 days, the numbers of peptide specific CD8⁺ T cells weremeasured using appropriate fluoresceinated peptide:HLA-A2 pentamers.These were analysed on a flow cytometer and expressed as % of gatedcells, excluding dead and CD14⁺ cells. Results for donor 5 (from table4) are shown; and

FIG. 6 shows functional CD8⁺ T cells recognising Rb7 can be detected inhealthy donors. Specifically, peripheral blood lymphocytes from HLA-A2⁺healthy donors were enriched for CD8+ T cells, then cultured for 14 dayswith Rb7 peptide and antigen presenting cells (APC). The cultured cellswere harvested and tested in enzyme linked immunospot (ELISPOT) assaysto measure the numbers of T cells able to secrete IFN-□ in response toRb7 peptide. Three (A, B, C) out of seven donors were capable of makingsignificant responses (number of spots for T cells+Rb7+PBMC>2 standarddeviations above T cells+PBMC).

EXAMPLE 1

Candidate 9 or 10 amino acid peptides from 15 proteins were selected foranalysis, see Table 4 for the full list of peptides. One hundred and twopeptides predicted to bind to HLA-A*0201 were selected according topublished algorithms (33,34). (Table 4). The algorithm we used has beenused previously to successfully predict other tumour-specific CTLepitopes (17). We chose HLA-A*0201 as the co-presenting peptide as thisis the most common HLA allele (˜40%) among Caucasians, and there arewell-defined in vivo and in vitro model systems to facilitate proof ofconcept experiments. From the initial list of 102 peptides, 62 weresynthesized for testing.

Peptides were Tested for Binding to HLA-A*0201.

CTL recognise peptides bound to HLA class I molecules on the cellsurface. Therefore peptides must demonstrate binding to HLA to beuseful. This can be measured by using a cell based assay measuring anincrease in HLA-A*0201 expression resulting from binding.

A cell-based peptide binding assay ((35)) was used to show that themajority (43/62) of candidate peptides could bind to HLA-A*0201 (Table3, FIG. 3).

HLA-A2 Binding of Host Protein Derived Peptides.

HLA-A*0201 expression of T2 cells was monitored by flow cytometry afterovernight incubation with 100 μg test peptides. Each peptide was testedin quadruplicate. A percentage increase in HLA-A*0201 expression ofabove 50% was considered significant.

The level of binding observed could be classified as either strong ormoderate, and was comparable to two well-known HLA-A*0201 restricted CTLepitopes (influenza M1 and EBV BMFL1)(FIG. 3).

43 of the peptides that showed a greater than 50% increase in HLA-A*0201expression were chosen as candidates for testing in immunogenicityexperiments.

Testing In Vivo Immunogenicity in Mice.

We have used HLA-A*0201 transgenic mice to test potential human vaccines(36). These mice can be immunised with peptides together with adjuvantto monitor development of in vivo responses. These responses weredetected using ELISPOT assays to measure the numbers of IFN-γ securingpeptide specific T cells in the spleen.

This was done with 20 peptides from the Rb(6), Mupp1 (7), BAK (3), DLG(2), AP (2) proteins. All peptides were chosen on the strength ofpeptide binding (FIG. 3). The M1₅₈₋₆₆ peptide from influenza, a knownHLA-A*0201 binder was used as a positive control. Significant T cellresponses were seen against the positive control M1₅₈₋₆₆ peptide (7/12mice) and a peptide from Rb₄₈₅₋₄₉₃ (Rb7) protein (7/10 mice). Theresults are shown in FIG. 4.

Testing In Vitro Immunogenicity using Human T Lymphocytes.

The candidate peptides must be capable of activating human T lymphocytesthat can recognise and kill cancer cells. We detected peptide specific Tcells in the peripheral blood of patients with cervical cancer. Thisproved the concept that such peptides can be immunogenic despite beingderived from “self” proteins.

Detection of Peptide Specific T Cells

T cells reactive against peptides of the invention should bepreferentially found in HLA-A2⁺ patients with cervical cancer. Bloodsamples from 4 patients (3 with cervical cancer, 1 with premalignantdisease, CIN3) were tested for the presence of CD8⁺ T cells recognisingRb7 peptide. Fluoresceinated multimeric HLA-A2/peptide complexes wereused to measure numbers of peptide specific T cells by flow cytometry(10). This assay demonstrated that T cells specific for Rb7 peptidecould be detected at low frequency in the blood of 2 patients withcervical cancer. These frequencies were similar to those previouslyobtained for HPV16 E7 peptide specific T cells (10). This suggests thatit should be possible to isolate and propagate Rb specific T cells forfurther experiments.

Using the technique described above, T lymphocytes recognising certain“self” tumour antigens such as melan-A can also be readily detected inhealthy donors (50). However it is usually the case that T lymphocytesrecognising “self” antigens are difficult to detect in healthy donors.Blood samples from 8 healthy donors (all HLA-A2+) were tested for thepresence of CD8⁺ T cells recognising Rb7 peptide and melan-A peptide,using appropriate fluoresceinated multimers (pentamers). T lymphocytesrecognising Rb7 peptide could be detected at variable but generally lowfrequencies in all 8 healthy donors (Table 6). By contrast T lymphocyteresponses against melan-A were extremely high frequency, confirmingprevious reports (50). The highest frequency of T lymphocytes specificfor Rb7 was found in donor 5 (FIG. 5).

The assays described above demonstrate that human T cells recognisingRb7 can be detected in both patients and healthy donors. ELISPOT assayswere used to determine whether Rb7 peptide specific CD8⁺ T lymphocytescultured from healthy donors, were capable of secreting IFN-γ. Sevenhealthy donors were tested, with 3 donors demonstrating detectablenumbers of IFN-γ secreting T lymphocytes (FIG. 5).

Overall these results suggest that host cell protein fragments producedby HPV processing, such as the Rb7 peptide, is immunogenic for humanCD8⁺ T lymphocytes, and can elicit functional (IFN-γ secretion)responses. This suggests that it should be possible to isolate andpropagate large numbers of Rb specific T cells for either experimentalor clinical therapeutic use. Full List of HLA Class I alleles assignedas of July 2005 HLA-A HLA-B HLA-C HLA-E HLA-F HLA-G A*01010101 B*070201Cw*010201 E*01010101 F*010101 G*010101 A*01010102N B*070202 Cw*010202E*01010102 F*010102 G*010102 A*010102 B*070203 Cw*010203 E*01030101G*010103 A*010103 B*070204 Cw*0103 E*01030102 G*010104 A*0102 B*0703Cw*0104 E*010302 G*010105 A*0103 B*0704 Cw*0105 E*010303 G*010106A*0104N B*0705 Cw*0106 E*010304 G*010107 A*0106 B*0706 Cw*0107 E*0104G*010108 A*0107 B*0707 Cw*0108 G*0102 A*0108 B*0708 Cw*0109 G*0103A*0109 B*0709 Cw*0110 G*010401 A*0110 B*0710 Cw*0111 G*010402 A*0111NB*0711 Cw*020201 G*010403 A*0112 B*0712 Cw*020202 G*0105N A*0113 B*0713Cw*020203 G*0106 A*0114 B*0714 Cw*020204 A*0115N B*0715 Cw*020205A*02010101 B*0716 Cw*0203 A*02010102L B*0717 Cw*0204 A*020102 B0718Cw*0205 A*020103 B*0719 Cw*0206 A*020104 B*0720 Cw*0207 A*020105 B*0721Cw*0208 A*020106 B*0722 Cw*0209 A*020107 B*0723 Cw*0210 A*020108 B*0724Cw*0211 A*020109 B*0725 Cw*0212 A*020110 B*0726 Cw*030201 A*020111B*0727 Cw*030202 A*0202 B*0728 Cw*030301 A*020301 B*0729 Cw*030302A*020302 B*0730 Cw*030303 A*0204 B*0731 Cw*030304 A*0205 B*0732Cw*030401 A*020601 B*0733 Cw*030402 A*020602 B*0734 Cw*030403 A*020603B*0735 Cw*0305 A*0207 B*0736 Cw*0306 A*0208 B*0737 Cw*0307 A*0209 B*0738Cw*0308 A*0210 B*0739 Cw*0309 A*0211 B*0740 Cw*0310 A*0212 B*0741Cw*0311 A*0213 B*0742 Cw*0312 A*0214 B*0743 Cw*0313 A*0215N B*080101Cw*0314 A*0216 B*080102 Cw*0315 A*021701 B*0802 Cw*0316 A*021702 B*0803Cw*0317 A*0218 B*0804 Cw*0318 A*0219 B*0805 Cw*0319 A*022001 B*0806Cw*04010101 A*022002 B*0807 Cw*04010102 A*0221 B*0808N Cw*040102 A*0222B*0809 Cw*040103 A*0224 B*0810 Cw*0403 A*0225 B*0811 Cw*040401 A*0226B*0812 Cw*040402 A*0227 B*0813 Cw*0405 A*0228 B*0814 Cw*0406 A*0229B*0815 Cw*0407 A*0230 B*0816 Cw*0408 A*0231 B*0817 Cw*0409N A*0232NB*0818 Cw*0410 A*0233 B*0819N Cw*0411 A*0234 B*0820 Cw*0412 A*023501B*0821 Cw*0413 A*023502 B*0822 Cw*0414 A*0236 B*0823 Cw*0415 A*0237B*0824 Cw*0416 A*0238 B*0825 Cw*0417 A*0239 B*1301 Cw*050101 A*0240B*130201 Cw*050102 A*0241 B*130202 Cw*0502 A*0242 B*1303 Cw*0503 A*0243NB*1304 Cw*0504 A*0244 B*1306 Cw*0505 A*0245 B*1307N Cw*0506 A*0246B*1308 Cw*0507N A*0247 B*1309 Cw*0508 A*0248 B*1310 Cw*0509 A*0249B*1311 Cw*0510 A*0250 B*1312 Cw*0511 A*0251 B*1313 Cw*0602 A*0252 B*1401Cw*0603 A*0253N B*140201 Cw*0604 A*0254 B*140202 Cw*0605 A*0255 B*1403Cw*0606 A*0256 B*1404 Cw*0607 A*0257 B*1405 Cw*0608 A*0258 B*140601Cw*0609 A*0259 B*140602 Cw*0610 A*0260 B*1407N Cw*0611 A*0261 B*15010101Cw*0612 A*0262 B*15010102N Cw*0613 A*0263 B*150102 Cw*070101 A*0264B*150103 Cw*070102 A*0265 B*150104 Cw*070103 A*0266 B*150105 Cw*07020101A*0267 B*1502 Cw*07020102 A*0268 B*1503 Cw*07020103 A*0269 B*1504Cw*0703 A*0270 B*1505 Cw*070401 A*0271 B*1506 Cw*070402 A*0272 B*1507Cw*0705 A*0273 B*1508 Cw*0706 A*027401 B*1509 Cw*0707 A*027402 B*1510Cw*0708 A*0275 B*151101 Cw*0709 A*0276 B*151102 Cw*0710 A*0277 B*1512Cw*0711 A*0278 B*1513 cw*0712 A*0279 B*1514 Cw*0713 A*0280 B*1515Cw*0714 A*0281 B*1516 Cw*0715 A*0282N B*15170101 Cw*0716 A*0283NB*15170102 Cw*0717 A*0284 B*151702 Cw*0718 A*0285 B*1518 Cw*0719 A*0286B*1519 Cw*0720 A*03010101 B*1520 Cw*0721 A*03010102N B*1521 Cw*0722A*03010103 B*1523 Cw*0723 A*030102 B*1524 Cw*0724 A*030103 B*1525Cw*0725 A*030104 B*1526N Cw*0726 A*0302 B*1527 Cw*0727 A*0303N B*1528Cw*0728 A*0304 B*1529 Cw*0729 A*0305 B*1530 Cw*0730 A*0306 B*1531Cw*080101 A*0307 B*1532 Cw*080102 A*0308 B*1533 Cw*0802 A*0309 B*1534Cw*0803 A*0310 B*1535 Cw*0804 A*0311N B*1536 Cw*0805 A*0312 B*1537Cw*0806 A*0313 B*1538 Cw*0807 A*0314 B*1539 Cw*0808 A*0315 B*1540Cw*0809 A*0316 B*1542 Cw*0810 A*0317 B*1543 Cw*0811 A*110101 B*1544Cw*0812 A*110102 B*1545 Cw*120201 A*110103 B*1546 Cw*120202 A*110104B*1547 Cw*120203 A*110105 B*1548 Cw*120301 A*1102 B*1549 Cw*120302A*1103 B*1550 Cw*120303 A*1104 B*1551 Cw*120401 A*1105 B*1552 Cw*120402A*1106 B*1553 Cw*1205 A*1107 B*1554 Cw*1206 A*1108 B*1555 Cw*1207 A*1109B*1556 Cw*1208 A*1110 B*1557 Cw*1209 A*1111 B*1558 Cw*1210 A*1112 B*1560Cw*1211 A*1113 B*1561 Cw*1212 A*1114 B*1562 Cw*1213 A*1115 B*1563Cw*1214 A*1116 B*1564 Cw*1215 A*1117 B*1565 Cw*140201 A*1118 B*1566Cw*140202 A*1119 B*1567 Cw*140203 A*1120 B*1568 Cw*140204 A*1121N B*1569Cw*1403 A*1122 B*1570 Cw*1404 A*1123 B*1571 Cw*1405 A*2301 B*1572Cw*1406 A*2302 B*1573 Cw*1407N A*2303 B*1574 Cw*150201 A*2304 B*1575Cw*150202 A*2305 B*1576 Cw*1503 A*2306 B*1577 Cw*1504 A*2307N B*1578Cw*150501 A*2308N B*1579N Cw*150502 A*2309 B*1580 Cw*150503 A*2310B*1581 Cw*150504 A*2311N B*1582 Cw*1506 A*2312 B*1583 Cw*1507 A*24020101B*1584 Cw*1508 A*24020102L B*1585 Cw*1509 A*240202 B*1586 Cw*1510A*240203 B*1587 Cw*1511 A*240204 B*1588 Cw*1512 A*240205 B*1589 Cw*1513A*240206 B*1590 Cw*1514 A*240301 B*1591 Cw*160101 A*240302 B*1592Cw*160102 A*2404 B*1593 Cw*1602 A*2405 B*1594N Cw*160401 A*2406 B*1595Cw*1606 A*2407 B*1596 Cw*1607 A*2408 B*1597 Cw*1701 A*2409N B*1598Cw*1702 A*2410 B*1599 Cw*1703 A*2411N B*180101 Cw*1801 A*2413 B*180102Cw*1802 A*2414 B*1802 A*2415 B*1803 A*2417 B*1804 A*2418 B*1805 A*2419B*1806 A*2420 B*1807 A*2421 B*1808 A*2422 B*1809 A*2423 B*1810 A*2424B*1811 A*2425 B*1812 A*2426 B*1813 A*2427 B*1814 A*2428 B*1815 A*2429B*1817N A*2430 B*1818 A*2431 B*1819 A*2432 B*1820 A*2433 B*2701 A*2434B*2702 A*2435 B*2703 A*2436N B*270401 A*2437 B*270402 A*2438 B*270502A*2439 B*270503 A*2440N B*270504 A*2441 B*270505 A*2442 B*270506 A*2443B*270507 A*2444 B*270508 A*2445N B*270509 A*2446 B*2706 A*2447 B*2707A*2448N B*2708 A*2449 B*2709 A*2450 B*2710 A*2451 B*2711 A*2452 B*2712A*2453 B*2713 A*250101 B*2714 A*250102 B*2715 A*2502 B*2716 A*2503B*2717 A*2504 B*2718 A*260101 B*2719 A*260102 B*2720 A*260103 B*2721A*260104 B*2723 A*2602 B*2724 A*2603 B*2725 A*2604 B*2726 A*2605 B*2727A*2606 B*2728 A*260701 B*2729 A*260702 B*2730 A*2608 B*350101 A*2609B*350102 A*2610 B*350103 A*2611N B*350104 A*2612 B*350201 A*2613B*350202 A*2614 B*3503 A*2615 B*350401 A*2616 B*350402 A*2617 B*3505A*2618 B*3506 A*2619 B*3507 A*2620 B*3508 A*2621 B*350901 A*2622B*350902 A*2623 B*3510 A*2624 B*3511 A*2625N B*3512 A*2626 B*3513A*29010101 B*351401 A*29010102N B*351402 A*290201 B*3515 A*290202 B*3516A*290203 B*3517 A*2903 B*3518 A*2904 B*3519 A*2905 B*3520 A*2906 B*3521A*2907 B*3522 A*2908N B*3523 A*2909 B*3524 A*2910 B*3525 A*2911 B*3526A*2912 B*3527 A*2913 B*3528 A*2914 B*3529 A*300101 B*3530 A*300102B*3531 A*300201 B*3532 A*300202 B*3533 A*300203 B*3534 A*3003 B*3535A*3004 B*3536 A*3006 B*3537 A*3007 B*3538 A*3008 B*3539 A*3009 B*3540NA*3010 B*3541 A*3011 B*3542 A*3012 B*3543 A*3013 B*3544 A*3014L B*3545A*3015 B*3546 A*310102 B*3547 A*3102 B*3548 A*3103 B*3549 A*3104 B*3550A*3105 B*3551 A*3106 B*3552 A*3107 B*3553N A*3108 B*3554 A*3109 B*3555A*3110 B*3556 A*3111 B*3557 A*3112 B*3558 A*3201 B*3559 A*3202 B*3560A*3203 B*3561 A*3204 B*3701 A*3205 B*3702 A*3206 B*3703N A*3207 B*3704A*3208 B*3705 A*3209 B*3706 A*3210 B*3707 A*3301 B*3708 A*330301 B*3709A*330302 B*3801 A*3304 B*380201 A*3305 B*380202 A*3306 B*3803 A*3307B*3804 A*3308 B*3805 A*3401 B*3806 A*3402 B*3807 A*3403 B*3808 A*3404B*3809 A*3405 B*3810 A*3406 B*3811 A*3601 B*39010101 A*3602 B*39010102LA*3603 B*390103 A*3604 B*390104 A*4301 B*390201 A*6601 B*390202 A*6602B*3903 A*6603 B*3904 A*6604 B*3905 A*680101 B*390601 A*680102 B*390602A*680103 B*3907 A*6802 B*3908 A*680301 B*3909 A*680302 B*3910 A*6804B*3911 A*6805 B*3912 A*6806 B*391301 A*6807 B*391302 A*6808 B*3914A*6809 B*3915 A*6810 B*3916 A*6811N B*3917 A*6812 B*3918 A*6813 B*3919A*6814 B*3920 A*6815 B*3922 A*6816 B*3923 A*6817 B*3924 A*6818N B*3925NA*6819 B*3926 A*6820 B*3927 A*6821 B*3928 A*6822 B*3929 A*6823 B*3930A*6824 B*3931 A*6825 B*3932 A*6826 B*3933 A*6827 B*3934 A*6828 B*400101A*6901 B*400102 A*7401 B*400103 A*7402 B*400104 A*7403 B*400105 A*7404B*400201 A*7405 B*400202 A*7406 B*400203 A*7407 B*4003 A*7408 B*4004A*7409 B*4005 A*7410 B*40060101 A*7411 B*40060102 A*8001 B*400602 B*4007B*4008 B*4009 B*4010 B*4011 B*4012 B*4013 B*401401 B*401402 B*401403B*4015 B*4016 B*4018 B*4019 B*4020 B*4021 B*4022N B*4023 B*4024 B*4025B*4026 B*4027 B*4028 B*4029 B*4030 B*4031 B*4032 B*4033 B*4034 B*4035B*4036 B*4037 B*4038 B*4039 B*4040 B*4042 B*4043 B*4044 B*4045 B*4046B*4047 B*4048 B*4049 B*4050 B*4051 B*4052 B*4053 B*4054 B*4055 B*4056B*4057 B*4058 B*4059 B*4060 B*4061 B*4101 B*4102 B*4103 B*4104 B*4105B*4106 B*4107 B*4201 B*4202 B*4204 B*420501 B*420502 B*4206 B*44020101B*44020102S B*440202 B*440203 B*440301 B*440302 B*4404 B*4405 B*4406B*4407 B*4408 B*4409 B*4410 B*4411 B*4412 B*4413 B*4414 B*4415 B*4416B*4417 B*4418 B*4419N B*4420 B*4421 B*4422 B*4423N B*4424 B*4425 B*4426B*4427 B*4428 B*4429 B*4430 B*4431 B*4432 B*4433 B*4434 B*4435 B*4436B*4437 B*4438 B*4439 B*4440 B*4441 B*4442 B*4501 B*4502 B*4503 B*4504B*4505 B*4506 B*4507 B*4601 B*4602 B*4603 B*4604 B*4605 B*47010101B*47010102 B*4702 B*4703 B*4704 B*4705 B*4801 B*4802 B*4803 B*4804B*4805 B*4806 B*4807 B*4808 B*4809 B*4810 B*4811 B*4812 B*4813 B*4901B*4902 B*4903 B*4904 B*5001 B*5002 B*5004 B*510101 B*510102 B*510103B*510104 B*510105 B*510106 B*510107 B*510201 B*510202 B*5103 B*5104B*5105 B*5106 B*5107 B*5108 B*5109 B*5110 B*5111N B*5112 B*511301B*511302 B*5114 B*5115 B*5116 B*5117 B*5118 B*5119 B*5120 B*5121 B*5122B*5123 B*5124 B*5126 B*5127N B*5128 B*5129 B*5130 B*5131 B*5132 B*5133B*5134 B*5135 B*5136 B*5137 B*5138 B*520101 B*520102 B*520103 B*520104B*5202 B*5203 B*5204 B*5205 B*5206 B*5207 B*5208 B*530101 B*530102B*530103 B*5302 B*5303 B*5304 B*5305 B*5306 B*5307 B*5308 B*5309 B*5310B*5401 B*5402 B*5403 B*5404 B*5405N B*5406 B*5407 B*550101 B*550102B*5502 B*5503 B*5504 B*5505 B*5507 B*5508 B*5509 B*5510 B*5511 B*5512B*5513 B*5514 B*5515 B*5516 B*5517 B*5518 B*5519 B*5601 B*5602 B*5603B*5604 B*560501 B*560502 B*5606 B*5607 B*5608 B*5609 B*5610 B*5611B*5612 B*5613 B*5614 B*5615 B*5616 B*570101 B*570102 B*570103 B*5702B*570301 B*570302 B*5704 B*5705 B*5706 B*5707 B*5708 B*5709 B*5801B*5802 B*5804 B*5805 B*5806 B*5807 B*5808 B*5809 B*5810N B*5811 B*5901B*670101 B*670102 B*6702 B*7301 B*7801 B*780201 B*780202 B*7803 B*7804B*7805 B*8101 B*8102 B*8201 B*8202 B*8301 B*9501 B*9502 B*9503 B*9504

TABLE 2 Monoclonal antibodies used to treat cancer, their target andmechanism of action. Name of monoclonal antibody Target/Mechanism ofaction Rituximab (Rituxan ®) Used to treat B-cell lymphomas, acts bybinding to the CD20 molecule present on all B cells. Herceptin ® Bindsto HER2, a growth factor receptor found on some tumour cells, such asbreast cancers and lymphomas. Alemtuzumab (MabCampath ®) Used to treatchronic lymphocytic leukaemia. Binds to the CD52 molecule found on allwhite blood cells. Lym-1 (Oncolym ®) Used to treat lymphoma. Binds tothe histocompatibility antigen found on lymphoma cells. Bevacizumab(Avastin ®) Used to treat tumours. Binds to vascular endothelial growthfactor, which is found in healthy as well as malignant cells. Cetuximab(Erbitux ®) Used to treat colorectal cancers. Binds to epidermal growthfactor receptor, which is also found on normal epithelial cells.Telomerase antibody Used to treat cancers in general. Binds totelomerase, which is the protein responsible for cancer cellsover-riding the usual apoptosis mechanisms. This protein is also presenton normal cells.

TABLE 3 Host cell proteins known to be targeted for degradationfollowing binding to HPV E6 or E7 proteins. Host cell HPV Gene Accessiontarget* protein Other names name number Function Location ReferenceRetinoblastoma E7 Retinoblastoma RB1 M15400 cell cycle Nuclear (19) 1susceptibility regulation, protein tumour suppressor E6AP E6 Human UBE3AAF002224 proteolysis; Cytosolic (24) papillomavirus E6 binds toassociated HPV16&18 protein E6 to target (E6AP), Ubiquitin p53 forprotein ligase degradation, E3A (UBE3A) can also target itself forubiquination and degradation C-MYC E6 v-myc MYC AY214166 cell cycle,Nuclear (25) myelocytomatosis gene viral oncogene transcription homolog(avian), myc protooncogene product HSCRIB E6 scribbled SCRIB AY062238cell cycle membrane (26) homologue, vartul HMCM7 E6 minichromosome MCM7AB004270 DNA nuclear (27) maintenance replication deficient 7, CDC47MAGI1 E6 membrane MAGI1 AB010894 Signalling, membrane (28) associatedtight guanylate kinase, junctions, WW and PDZ cell domain adhesioncontaining 1, BAIAP1, BAP1, MAGI-1, AIP3 SIPA1L1 E6 signal-inducedSIPA1L1 AB007900 GTPase membrane (29) proliferation- activatingassociated 1 like protein 1, E6 targetted protein 1 (E6TP1) DLG1 E6discs, large DLG1 U13897 cell growth, membrane (30) homolog 1 adhesion,(DLG1, HDLG), signalling synapse associated protein 97 (SAP97), hdlg BAKE6 BCL2- BAK1 U23765 proapoptotic, membrane (31) antagonist/killer 1 inpresence of appropriate stimuli binds to BCL-2 to accelerate cell deathMPDZ E6 multiple PDZ MPDZ AF093419 tight membrane (32) domain proteinjunction (MUPP1) formation MGMT E6 0-6- MGMT M29971 DNA repair nuclear(33) methylguanine- DNA methyltransferase MAGI-2 E6 membrane MAGI2AB014605 same as membrane (34) associated magi-1 guanylate kinase, WWand PDZ domain containing 2, activin receptor interacting protein 1(ARIP1) MAGI-3 E6 membrane MAGI3 AF213259 same as membrane (34)associated magi-1 guanylate kinase, WW and PDZ domain containing 3Tuberin E6 tuberous TSC2 AB014460 tumour membrane (35) sclerosis 2suppressor, (TSC2) GTPase signalling N-MYC E6 v-myc MYCN M13228 tumourmembrane (25) myelocytomatosis suppressor viral related oncogene, neuro-blastoma derived (avian), N-MYC proto-oncogene protein*Proteins are listed by their agreed standard names, rather than thepublished names.

TABLE 4 Host cell proteins and HLA-A*0201 binding peptides ProteinStarting Pos Sequence T0.5 Number Retinoblastoma 563 WLSDsPLFDL 5375 1Retinoblastoma 475 KLLNdNIFHM 858 2 Retinoblastoma 75 WLTWeKVSSV 736 3Retinoblastoma 646 SLSLFYKKV 396 4 Retinoblastoma 447 KLGVrLYYRV 365 5Retinoblastoma 218 LMLCvLDYFI 261 6 Retinoblastoma 485 SLLACALEV 257 7Retinoblastoma 157 VLFALFSKL 255 8 Retinoblastoma 648 SLFYkKVYRL 182 9Retinoblastoma 824 KMTPrSRILV 176 10 Retinoblastoma 679 IIWTIFQHTL 15711 Retinoblastoma 188 ALVLKVSWI 132 12 Retinoblastoma 76 LTWEKVSSV 12913 Retinoblastoma 703 IMMCSMYGI 109 14 Retinoblastoma 900 KLAEmTSTRT 10715 Retinoblastoma 219 MLCVLDYFI 98 16 BAK 150 FLGQvTRFVV 761 17 BAK 129ALLGFGYRL 300 18 BAK 188 ILNVIVVLGV 272 19 BAK 182 NLGNgPILNV 160 20 BAK195 VVLLGQFVV 91 21 BAK 191 VLVVIGVVLL 84 22 BAK 145 GLTGFLGQV 79 23 DLG355 ALYDRLADV 2099 24 DLG 275 NLHGvFVAEV 608 25 DLG 345 GLPGDSFYI 333 26DLG 148 QLLEfNGINL 324 27 DLG 666 VLWIPACPL 301 28 DLG 497 VLILgPLLDV272 29 DLG 301 LILEyGSLDV 247 30 DLG 480 SLAYqRVQKV 160 31 DLG 498LILGPLLDV 138 32 DLG 178 ILAQYNPHV 118 33 E6AP 127 YLTEeKVYEI 453 34E6AP 449 FINEPLNEV 415 35 E6AP 748 YLFRpEEIEL 364 36 E6AP 657 VLYQSLKDL267 37 E6AP 785 VLIREFWEI 253 38 E6AP 226 KLGPDDVSV 243 39 E6AP 283YLNLFIIGM 200 40 E6AP 785 VLIReFWEIV 153 41 E6AP 477 FMTCpFILNA 144 42E6AP 262 YLSPnVECDL 98 43 C-MYC 133 CMWSgFSAAA 113 44 C-MYC 68GLCSpSYVAV 104 45 C-MYC 177 YLQDLSAAA 94 46 C-MYC 133 CMWSGFSAA 57 47MUPP1 745 LLPGdRLMFV 1496 48 MUPP1 692 AMWEaGIQHI 590 49 MUPP1 607LLGENHQDV 485 50 MUPP1 981 YLLEQSSLA 347 51 MUPP1 1650 LLGAiIIHEV 272 52MUPP1 814 GLADkPLFRA 272 53 MUPP1 606 TLLGeNHQDV 257 54 MUPP1 1547SLLKtAKMTV 257 55 MUPP1 1772 ILMVNGEDV 214 56 MUPP1 1524 KVGDQILAV 20157 MUPP1 1766 LMQGdQILMV 196 58 MUPP1 592 KLFSGDELL 136 59 MUPP1 87TLQNESFLL 124 60 MUPP1 312 GMSSeQVAQV 116 61 MUPP1 751 LMFVNDVNL 97 62E6TP1 855 SMGAIVWAV 867 63 E6TP1 886 VLIEqETKSV 485 64 E6TP1 960GLGQLGFHV 403 65 E6TP1 877 LLGIsNEFIV 281 66 E6TP1 1009 QMIDILRTSV 20667 E6TP1 1592 VLFSsTYPSL 202 68 E6TP1 783 FLLAKVINA 194 69 E6TP1 45SLGSsVMAPV 160 70 E6TP1 641 FLQLLGERV 157 71 E6TP1 339 ILFDLNEAI 132 72E6TP1 1522 KLIDLESPT 107 73 MAGI-1 69 LLLEvQGVRV 1794 75 MAGI-1 262TLQEtALPPV 656 76 MAGI-1 1054 KVGDRILAV 201 77 MAGI-1 161 FLTVkEFLDL 18778 MAGI-1 80 GLPRyDVLGV 160 79 MAGI-1 717 LLVQrGGLPV 118 80 MAGI-1 527VLGHTHAQV 118 81 MCM7 356 RLAQHITYV 880 82 MCM7 335 LLSRfDLLWL 459 83MCM7 60 KMQEHSDQV 353 84 MCM7 259 VLADqGVCCI 167 85 MCM7 439 ALARIRMVDV160 86 MCM7 381 KLMRrYIAMC 148 87 MCM7 178 LLLLLVGGV 131 88 MCM7 481ALDEyEELNV 114 89 MCM7 273 KMAEaDRTAI 108 90 Vartul 713 KLLEvNGVAL 113491 Vartul 99 SLPAsLSFLV 403 92 Vartul 348 YLLPQQPPL 364 93 Vartul 229ILTEnLLMAL 342 94 Vartul 244 KLTKITNLNV 243 95 Vartul 15 FMQLVELDV 23196 Vartul 1199 KLDYrALAAV 224 97 Vartul 68 ALNDvSLQAL 201 98 Vartul 63SLAHIALNDV 160 99 Vartul 992 ILAVNGQDV 118 100 Vartul 849 VLSINGVDV 118101 Vartul 129 ALPNIRELWL 117 102 MGMT 98 VLWKLLKVV 925 MGMT 161GLAVKEWLL 160 MGMT 167 WLLAhEGHRL 364 MGMT 89 FQQEsFTRQV 101 N-Myc 421VILKkATEYV 162 440 LLLEkEKLQA 128 446 KLQArQQQLL 75 MAGI-2 65 LLLEvNETPV1794 993 KLIKdAGLSV 243 970 KVGDRILAV 201 43 YLGEvKPGKV 171 76GLTIrDVLAV 160 528 AIMERPPPV 145 751 AIYESRQQV 125 481 VLGHTHADV 118 639GLCEGDLIV 117 65 LLLEvNETPV 1794 993 KLIKdAGLSV 243 970 KVGDRILAV 201 43YLGEvKPGKV 171 76 GLTIrDVLAV 160 528 AIMERPPPV 145 751 AIYESRQQV 125 481VLGHTHADV 118 639 GLCEGDLIV 117 MAGI-3 70 VLLEvNGTPV 1794 502 FQLVpVNQYV660 503 QLVPVNQYV 383 11 WLSKvQECAV 320 923 KVGDHISAV 201 726 KLDPSEVYL164 654 NLTHIQVVEV 160 200 FQPDPVDQV 150 1067 NMGLFILRL 135 1121LLLLrPGTGL 134 1122 LLLRPGTGL 134 499 VQMFQLVPV 102 70 VLLEvNGTPV 98 502FQLVpVNQYV 91 503 QLVPVNQYV 85 11 WLSKvQECAV 79 Tuberin 464 KVLDVLSFV4088 176 FLLVLVNLV 2723 1060 WLVGnKLVTV 736 291 LLRGAVFFV 659 1702IVSDrNLPFV 537 80 ALWKAVADL 408 1208 WLMSLENPL 364 688 LLFRvLLQCL 309117 GVLRaLFFKV 248 1065 KLVTVTTSV 243 464 KVLDvLSFVL 236 155 YLEEeLADFV226 258 KLMRNLLGT 222 1033 YVFSNFTAV 197 235 SLPLFIVTL 187 612LQAFdFLFLL 187 617 FLFLIRADSL 178 506 KLATqLLVDL 172 360 ILLNIIERL 151

TABLE 5 Summary of peptide binding No. peptides Source protein bindingBAK 6/7 DLG  7/10 CMYC 2/4 E6AP  9/10 MUPP1 13/15 Retinoblastoma  6/16Total 43/62

TABLE 6 Frequency of CD8⁺ T cells recognising Rb peptide in healthyvolunteers. Peripheral blood lymphocytes from HLA-A2⁺ healthy donorswere enriched for CD8⁺ T cells, then cultured for 14 days with Rb7peptide and antigen presenting cells (APC) or Melan-A (Mart1₂₆₋₃₅)peptide. Cells were harvested and tested with HLA-A2/Rb7 pentamer orHLA-A2/Melan-A pentamer. The numbers of CD8⁺ pentamer⁺ T lymphocyteswere measured by flow cytometry, excluding dead and CD14⁺ cells.Frequency of CD8⁺ pentamer⁺ cells Donor Rb Melan A 1 1/2500  1/24 21/1000 1/4 3 1/1000 1/3 4 1/909  1/3 5 1/120  1/4 6 1/3333  1/208 71/2000 1/3 8 1/2500 1/3

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1. A vaccine comprising: at least one isolated, purified, synthesised orrecombinant peptide, wherein the peptide is a fragment of a host cellprotein that has been degraded by a human papillomavirus (HPV)oncoprotein, and can elicit a cytotoxic T-lymphocyte (CTL) response whenadministered to a mammal.
 2. A vaccine according to claim 1, wherein themammal is human.
 3. A vaccine according to claim 1, wherein theoncoprotein is E6 or E7.
 4. A vaccine according to claim 1, wherein thehost cell protein comprises one or more of the proteins shown in Table3.
 5. A vaccine according to claim 1, wherein the peptide isHPV-specific or tumour-specific, meaning that it is presented in highamounts on the cell surface of HPV transformed or tumour cells, relativeto normal cells.
 6. A vaccine according to claim 5, wherein the peptideis 9-30 amino acids in length.
 7. A vaccine according to claim 6,wherein the peptide is 9-11 amino acids in length.
 8. A vaccineaccording to claim 7, wherein said vaccine comprises one or more of thepeptides shown in Table 4 (SEQ ID NOS: 1-163).
 9. A vaccine according toclaim 1, wherein the CTL response is HPV-specific or tumour-specific,meaning that the CTL can recognise HPV-transformed cells or tumour cellsexpressing the peptide of said vaccine.
 10. A vaccine according toclaims 1, 3, 4, 5, 8, or 9, which further comprises a majorhistocompatibility complex molecule.
 11. A vaccine according to claim10, wherein the major histocompatibility complex molecule is a class Imolecule.
 12. A vaccine according to claim 10, wherein the majorhisto-compatibility complex molecule is a human leucocyte antigen (HLA).13. A vaccine according to claim 10, wherein the majorhistocompatibility complex molecule comprises one or more of those shownin Table
 1. 14. A vaccine comprising: at least one isolated, purified,synthesised or recombinant peptide, wherein the peptide is chosen fromthose listed in Table
 4. 15. A vaccine comprising: at least oneisolated, purified, synthesised or recombinant peptide selected fromTable 4 and, further at least one isolated, purified, synthesised orrecombinant HLA selected from those listed in Table
 1. 16. A vaccinecomprising: at least one isolated, purified, synthesised or recombinantnucleic acid molecule encoding a peptide according to the vaccine of anyof claims 1-9 or 14 or peptide/HLA complex according to the vaccine ofany of claims 11-13 or
 15. 17. A vaccine according to claim 16, whereinthe nucleic acid molecule is in a vector and comprises a recombinantconstruct.
 18. A vaccine according to claim 17, wherein the construct isadapted for the expression of said peptide or peptide/HLA complex in aselected host system.
 19. A vector comprising a nucleic acid moleculeencoding a peptide selected from those listed in Table 4, andoptionally, an HLA selected from those listed in Table
 1. 20. A hostcell transformed or transfected by a vector according to claim
 19. 21. Acell, plasmid, virus, live organism or other vehicle having incorporatedexpressibly therein a nucleic acid molecule encoding a peptide selectedfrom those listed in Table 4 and optionally, an HLA selected from thoselisted in Table
 1. 22. A method of manufacturing a vaccine, which methodcomprises: culturing a host cell transformed or transfected with avector according to claim 19; and isolating/purifying the resultingconstruct product.
 23. A method of identifying HPV-specific ortumour-specific CTL, or the CTL receptors thereof, comprising: (a)culturing a sample containing CTL with at least one peptide thatrepresents a fragment of a host cell protein that is degraded by HPVproteins when said host cell is transformed or transfected by HPV,whereby said peptide is ultimately presented on a surface of avirally-infected cell; and (b) selecting CTL that recognise said peptideby binding thereto and, where the CTL receptor is to be identified,determining the nature of the receptor that binds said peptide.
 24. Amethod according to claim 23, wherein the peptide is selected from thoseshown in Table
 4. 25. A method according to claim 23 or claim 24,wherein the CTL are CD8⁺ cells.
 26. The use of a vaccine according toany one of claims 1-18 to treat HPV-associated diseases.
 27. The use ofa vaccine according to claim 26, wherein the disease is any one of thefollowing: cervical cancer, head and neck squamous cell cancer,non-melanoma skin cancers, liver cancer, mesothioloma or prostatecancer.
 28. A method of treatment, which method comprises administeringa vaccine according to any one of claims 1-18, to a mammal to betreated.
 29. A method according to claim 28, wherein the mammal ishuman.
 30. A peptide, or nucleic acid molecule encoding same, selectedfrom the list shown in Table
 4. 31. The use of a peptide according toclaim 30 as a vaccine.
 32. A complex comprising: at least one of thepeptides shown in Table 4, in association with an HLA co-presentingpeptide.
 33. A complex according to claim 32, wherein the HLA peptide isselected from those shown in Table
 1. 34. A complex according to claim32, wherein the HLA peptide is HLA-A binding protein.
 35. A complexaccording to any one of claims 32-34, wherein the HLA peptide is HLA-A0201.
 36. The use of an HPV-specific peptide for the production of anHPV vaccine, wherein said peptide is a fragment of a mammalian cellprotein that has been degraded by a human papillomavirus oncoprotein andwhich is presented, in combination with HLA, at the surface of thetransformed or transfected HPV cell, whereby the recognition of thispeptide HLA complex by a CTL results in the elicitation of an immuneresponse.